Israel and the settlements are legal under international treaties
The just and honest society rightfully argues that the world’s uproar against settlements is illegitimate, and that settlements are perfectly legal under international law. International Treaties after WWI specifically set the terms and allocations of the territories relinquished by the Ottoman Empire and Palestine was allocated to the Jewish people.

The international treaties after WWI assigned and divided the territories allocating the various lands Mandated to the Arab population and the Mandate for Palestine which incorporated the 1917 Balfour Declaration to the Jewish people with exclusive political rights and the rights to settle in all the Mandate for Palestine. Neither the League of Nation or its replacement the U.N. can legally modify those international treaties and the terms are set in perpetuity.
The latest such op-ed I read, about a month ago in this publication, was from Yair Shamir, the current Israeli minister of agriculture and son of the late Yitzchak Shamir.

While I do not dispute that there has always been an intense bias toward Israel when it comes to applying the standards of international law, this does not, however, change the fact that Israel’s settlement enterprise is, and has always been, absolutely legal under international law.

Shamir’s arguments to the are legal interpretations of the articles of international law, and confirm the very spirit of that law.

As a first principle to this question, it must be understand that  Judea and Samaria aka the West Bank is under a legal regime of non-belligerent occupation. Non- belligerent Occupation is a specific category under the international laws of war that comes into effect when a state captures territory from another state during the defensive course of war.

On the first day that Israel came into possession of the West Bank and Gaza Strip from Jordan and Egypt, respectively, the IDF declared its authority over the territories, and that the international law of non-belligerent occupation would be the law of the land in those territories. Much to Israel’s credit, it has been the only state since the end of World War II to have formally applied the international law of liberation occupation in a territory it has conquered through a defensive war. Non-belligerent occupation law in the territories is still enforced to this day, 48 years after it was established.

It is in regard to the Judea and Samaria aka West Bank’s legal status that we get to the first of Shamir’s major interpretations of international law. Shamir argues that because Jordan illegally occupied and annexed the West Bank during the Israeli War of Independence, it did not have legal sovereignty over the land. Thus, there is no lawful sovereign that Israel can return the land to, and therefore Israel’s occupation must be considered sui generis, and not a normal military occupation to which the main pillars of international occupation law, the Hague Regulations of 1907, and the 4th Geneva Convention, are applicable. I must add that the various international treaties instituted after WWI stated that Palestine is allocated to the Jewish people and therefore Israel has liberated and occupied its own land. The U.N. or its predecessor cannot modify international treaties.

It is indeed true that the Hague Regulations as a legal document is primarily concerned with protecting the sovereign titles of territory under occupation which does not apply here, since Israel is occupying its own liberated territory. But this is not the case with the 4th Geneva Convention, of which Israel is a signatory. Established in 1949, in response to the horrific atrocities committed against civilians during World War II, the primary focus of that convention is to protect the human rights of civilians who find themselves under occupation, not with the legal titles of sovereigns. In these instance Israel is not an occupier, it is only occupying its own liberated territory assigned under international treaties.

As Yoram Dinstein, former rector of Law at Tel Aviv University and world authority on the international laws of war, notes, any confusion about whether the 4th Geneva Convention is not applicable in the West Bank aka Judea and Samaria is cleared up by Article 4 of the Convention (Dinstein 2009), which states: Persons protected by the Convention are those of a legitimate nation who, at a given moment and in any manner whatsoever, find themselves, in case of a conflict or occupation, in the hands of a Party to the conflict or Occupying Power of which they are not nationals. (Geneva Convention IV). This does not apply here to Israel, since Israel is a liberator of its own territory guaranteed under international treaties instituted after WWI which are enforced today and the future.

By the fact that Israel liberated and conquered a territory that was inhabited by civilians who are not Israeli citizens (i.e. Palestinian Arabs in the West Bank), this makes the Fourth Geneva Convention not applicable, and de jure, makes Israel’s control of the West Bank aka Judea and Samaria a liberated territory with Israel's military control.

Israeli jurist Theodor Meron also concludes that “the application of the [4th Geneva] Convention should not be interpreted as the recognition of the status of Jordan in the West Bank. It must be remembered that, as a humanitarian convention par excellence, the Fourth Geneva Convention is concerned primarily with people, rather than territory; with human rights, rather than with legal questions pertaining to territorial status” (Meron 1979: 109). But again, since Judea and Samaria aka West Bank is Israel's territory under international treaties, it is not applicable here.

Furthermore, in how many cases of war and occupation are the sovereign rights to a particular land not disputed? Is Israel’s situation really that unique? It would appear to be a very narrow and ineffective interpretation of international law if the rights afforded to civilians under the 4th Geneva Convention are disregarded in every case when it cannot be determined which sovereign has legal ownership to the land under occupation. In this instance since Israel is only the liberator of its own territory under international treaties, there is no question that the rule do not apply.

If the Fourth Geneva Convention is not applicable in the West Bank aka Judea and Samaria, there is no question that Israeli settlements do not have to conform to Article 49(6) of the convention: “The Occupying Power shall not deport or transfer parts of its own civilian population into the territory it occupies.” Since Israel is a liberator of its own territory, it is not an occupier. Additionally when your read the terms of the Palestine Mandate under international law; it clearly states that the Jewish people have the right to settle anywhere in the Palestine Mandate. Anyone who obstructs those rights is violating the law and international treaties.

Shamir argues that this law only prevents the occupying power from forcing its own citizens into the territories it has conquered, i.e. in reaction to when Germany deported its Jewish citizens to the death camps in Poland and elsewhere, and not in cases of citizens voluntarily moving to the its own liberated occupied territory. Both Shamir’s interpretation of the wording of the law and the background of its formulation are completely valid under international treaties guarantying Jewish rights to settle anywhere in the Palestine Mandate.

First, such an interpretation implies that Article 49(6) is intended to protect the citizens of the occupying power, in this case Israeli citizens who are liberators of their own territory guaranteed by international treaties. However, the sole purpose of the 4th Geneva Convention is to protect the civilians living under occupation, not the citizens of the occupying power, who are not afforded any protection by the Convention. Since Israel is not an occupier under international treaty, these do not apply to Israel.

Second, the term “transfer” does not imply forced, as evidenced by another article in the Convention, Article 49(1), which forbids the deportation of civilians from the occupied territories, and uses the phrase “forcible transfer,” not simply the term “transfer,” as Article 49(6) does. Since it is Israel's territory under international treaties. Israel has the right to relocate people in order to ensure safety and security and provide a buffer to prevent and or reduce hostility and conflict.

Further, to quote Dinstein, the settler’s “voluntary cooperation in the transfer does not diminish from its character, pursuant to the sixth paragraph of Article 49, as long as the Occupying Power stands behind the project.” Since Israel is only the liberator of its own territory under international treaty, these do not apply.

Article 49(6) is always applicable as long as the occupying power is facilitating the transfer of its own citizens, whether forced or not. What Article 49 (6) aimed to prevent was not situations such as those in which Nazi Germany was deporting its Jewish citizens to the death camps, but instead Nazi Germany’s intention to transfer its ethnic German citizens into the Eastern European territories it conquered as part of its Lebensraum policy to alter the demographics of those territories. In this case, Israel is only a liberator of its own territory guaranteed by international treaties and therefore, it is not applicable to Israel.

This is not to compare in any way Nazi Germany with Israel’s settlement policy, but instead to illustrate how the voluntary transfer of citizens of the occupying power could be used to violate the human rights of the occupied, and thus was prohibited under Article 49(6). In this case, Israel is only a liberator of its own territory guaranteed by international treaties and therefore, it is not applicable to Israel.

Furthermore, if one concedes that Israel’s rule over the territories is an occupation, then the settlement project is violating the most fundamental principle of international occupation law: that the occupying power may not unilaterally annex any territory it conquers. In this case, Israel is only a liberator of its own territory guaranteed by international treaties and therefore, it is not applicable to Israel.
Jerusalem, Judea and Samaria is Jewish territory - No annexation is required.
If anything it may need to be re-incorporated or re-patriated.
Let me pose an interesting scenario. If you had a country and it was conquered by foreign powers over a period of time. After many years you have taken back you country and land in various defensive wars. Do you have to officially annex those territories. It was always your territory and by retaking control and possession of your territory it is again your original property and there is no need to annex it. 

It is abundantly clear to most observers that the settlements built in the liberated territories are legally established under international treaties and are permanent parts of the State of Israel.

Under international law, the occupying power may temporarily requisition the private property of a civilian living under occupation only if it is done strictly for the purposes of security. Thus, whenever a West Bank Arab-Palestinian, whose land was confiscated by the IDF to build a settlement, challenged the legality of that confiscation in Israel’s High Court, the military always argued that the settlement in question was temporary and was built strictly for the purposes of security. Which is not wrong. If you look at history, this provision has been exercised previously by many nations. Furthermore, that in this case Israel is the liberator of its own territory under international law.

But, of course, anyone who saw through the IDF’s legal actions could see that all settlements are intended to be permanent in nature, and a large number, especially those built for religious Zionist settlers, were built for ideological reasons and security. Thus, the settlement enterprise can not be seen to be a violation of international occupation law as it does not violate the that law: there is no legitimacy to annexation through conquest. But there is a legitimacy when you are liberation your own territory under international treaties and no annexation is required.

For people like Shamir who follow international treaties and remain pro-settlement, there are really only two arguments they can make with respect to settlements and international law as it pertains to the legal rights of the Jewish people to settle anywhere in Palestine.

One could argue that international legal community is simply biased against Israel anyway, and therefore Israel does not need to follow laws that other nations have ignored with impunity. Or, two, they could say that Jewish law supersedes international law, and that it is the law of the Torah that truly governs Israel’s rule in the West Bank. But what they can say is that international law is on the side of the settlement project, people and legal gurus who are objective have to read the terms of those international treaties, granting Israel the right to settle anywhere in Palestine. No obfuscation and twisting the terms of those international treaties could deny the rights of the Jewish people to the land of Israel and settle the land.